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-rw-r--r--wqflask/base/anon_collection.py21
-rw-r--r--wqflask/base/data_set.py349
-rw-r--r--wqflask/base/mrna_assay_tissue_data.py66
-rw-r--r--wqflask/base/species.py107
-rw-r--r--wqflask/base/template.py123
-rw-r--r--wqflask/base/trait.py356
-rw-r--r--wqflask/base/trait_collection.py53
-rw-r--r--wqflask/base/webqtlCaseData.py17
-rw-r--r--wqflask/base/webqtlConfig.py59
-rw-r--r--wqflask/base/webqtlFormData.py352
10 files changed, 313 insertions, 1190 deletions
diff --git a/wqflask/base/anon_collection.py b/wqflask/base/anon_collection.py
deleted file mode 100644
index 8ee73296..00000000
--- a/wqflask/base/anon_collection.py
+++ /dev/null
@@ -1,21 +0,0 @@
-class AnonCollection(TraitCollection):
-
- def __init__(self, anon_id)
- self.anon_id = anon_id
- self.collection_members = Redis.smembers(self.anon_id)
- print("self.collection_members is:", self.collection_members)
- self.num_members = len(self.collection_members)
-
-
- @app.route("/collections/remove", methods=('POST',))
- def remove_traits(traits_to_remove):
- print("traits_to_remove:", traits_to_remove)
- for trait in traits_to_remove:
- Redis.srem(self.anon_id, trait)
- members_now = self.collection_members - traits_to_remove
- print("members_now:", members_now)
- print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))
-
- # We need to return something so we'll return this...maybe in the future
- # we can use it to check the results
- return str(len(members_now))
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 54dd3c4b..ebf3f021 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -26,10 +26,10 @@ import collections
import codecs
import json
+import requests
import gzip
import cPickle as pickle
import itertools
-from operator import itemgetter
from redis import Redis
Redis = Redis()
@@ -44,8 +44,11 @@ from db import webqtlDatabaseFunction
from utility import webqtlUtil
from utility.benchmark import Bench
from utility import chunks
+from utility import gen_geno_ob
from utility.tools import locate, locate_ignore_error, flat_files
+from wqflask.api import gen_menu
+
from maintenance import get_group_samplelists
from MySQLdb import escape_string as escape
@@ -61,18 +64,21 @@ logger = getLogger(__name__ )
# Each subclass will add to this
DS_NAME_MAP = {}
-def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
+def create_dataset(dataset_name, rebuild=True, dataset_type = None, get_samplelist = True, group_name = None):
if not dataset_type:
dataset_type = Dataset_Getter(dataset_name)
logger.debug("dataset_type", dataset_type)
dataset_ob = DS_NAME_MAP[dataset_type]
dataset_class = globals()[dataset_ob]
- return dataset_class(dataset_name, get_samplelist)
+ if dataset_type == "Temp":
+ return dataset_class(dataset_name, get_samplelist, group_name)
+ else:
+ return dataset_class(dataset_name, get_samplelist)
class Dataset_Types(object):
- def __init__(self):
+ def __init__(self, rebuild=False):
"""Create a dictionary of samples where the value is set to Geno,
Publish or ProbeSet. E.g.
@@ -88,8 +94,10 @@ Publish or ProbeSet. E.g.
"""
self.datasets = {}
- if USE_GN_SERVER:
- data = menu_main()
+ if rebuild: #ZS: May make this the only option
+ data = json.loads(requests.get("http://gn2.genenetwork.org/api/v_pre1/gen_dropdown").content)
+ logger.debug("THE DATA:", data)
+ #data = gen_menu.gen_dropdown_json()
else:
file_name = "wqflask/static/new/javascript/dataset_menu_structure.json"
with open(file_name, 'r') as fh:
@@ -107,8 +115,9 @@ Publish or ProbeSet. E.g.
else:
new_type = "ProbeSet"
self.datasets[short_dataset_name] = new_type
+
# Set LOG_LEVEL_DEBUG=5 to see the following:
- logger.debugf(5,"datasets",self.datasets)
+ logger.debugf(5, "datasets",self.datasets)
def __call__(self, name):
return self.datasets[name]
@@ -166,20 +175,31 @@ def mescape(*items):
class Markers(object):
"""Todo: Build in cacheing so it saves us reading the same file more than once"""
def __init__(self, name):
- json_data_fh = open(locate(name + '.json','genotype/json'))
- try:
- markers = json.load(json_data_fh)
- except:
- markers = []
+ json_data_fh = open(locate(name + ".json",'genotype/json'))
+
+ markers = []
+ with open("%s/%s_snps.txt" % (flat_files('genotype/bimbam'), name), 'r') as bimbam_fh:
+ if len(bimbam_fh.readline().split(", ")) > 2:
+ delimiter = ", "
+ elif len(bimbam_fh.readline().split(",")) > 2:
+ delimiter = ","
+ elif len(bimbam_fh.readline().split("\t")) > 2:
+ delimiter = "\t"
+ else:
+ delimiter = " "
+ for line in bimbam_fh:
+ marker = {}
+ marker['name'] = line.split(delimiter)[0].rstrip()
+ marker['Mb'] = float(line.split(delimiter)[1].rstrip())/1000000
+ marker['chr'] = line.split(delimiter)[2].rstrip()
+ markers.append(marker)
for marker in markers:
- if (marker['chr'] != "X") and (marker['chr'] != "Y"):
+ if (marker['chr'] != "X") and (marker['chr'] != "Y") and (marker['chr'] != "M"):
marker['chr'] = int(marker['chr'])
marker['Mb'] = float(marker['Mb'])
self.markers = markers
- #logger.debug("self.markers:", self.markers)
-
def add_pvalues(self, p_values):
logger.debug("length of self.markers:", len(self.markers))
@@ -261,10 +281,12 @@ class DatasetGroup(object):
has multiple datasets associated with it.
"""
- def __init__(self, dataset):
+ def __init__(self, dataset, name=None):
"""This sets self.group and self.group_id"""
- #logger.debug("DATASET NAME2:", dataset.name)
- self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+ if name == None:
+ self.name, self.id, self.genetic_type = fetchone(dataset.query_for_group)
+ else:
+ self.name, self.id, self.genetic_type = fetchone("SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType FROM InbredSet where Name='%s'" % name)
if self.name == 'BXD300':
self.name = "BXD"
@@ -272,7 +294,6 @@ class DatasetGroup(object):
self.parlist = None
self.get_f1_parent_strains()
- self.accession_id = self.get_accession_id()
self.mapping_id, self.mapping_names = self.get_mapping_methods()
self.species = webqtlDatabaseFunction.retrieve_species(self.name)
@@ -282,55 +303,39 @@ class DatasetGroup(object):
self._datasets = None
self.genofile = None
- def get_accession_id(self):
- results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
- InbredSet.Name = %s and
- PublishFreeze.InbredSetId = InbredSet.Id and
- InfoFiles.InfoPageName = PublishFreeze.Name and
- PublishFreeze.public > 0 and
- PublishFreeze.confidentiality < 1 order by
- PublishFreeze.CreateTime desc""", (self.name)).fetchone()
-
- if results != None:
- return str(results[0])
- else:
- return "None"
-
def get_mapping_methods(self):
mapping_id = g.db.execute("select MappingMethodId from InbredSet where Name= '%s'" % self.name).fetchone()[0]
if mapping_id == "1":
- mapping_names = ["QTLReaper", "PYLMM", "R/qtl"]
+ mapping_names = ["GEMMA", "QTLReaper", "R/qtl"]
elif mapping_id == "2":
mapping_names = ["GEMMA"]
+ elif mapping_id == "3":
+ mapping_names = ["R/qtl"]
elif mapping_id == "4":
- mapping_names = ["PLINK"]
+ mapping_names = ["GEMMA", "PLINK"]
else:
mapping_names = []
return mapping_id, mapping_names
- def get_specified_markers(self, markers = []):
- self.markers = HumanMarkers(self.name, markers)
-
def get_markers(self):
- logger.debug("self.species is:", self.species)
-
def check_plink_gemma():
if flat_file_exists("mapping"):
MAPPING_PATH = flat_files("mapping")+"/"
- if (os.path.isfile(MAPPING_PATH+self.name+".bed") and
- (os.path.isfile(MAPPING_PATH+self.name+".map") or
- os.path.isfile(MAPPING_PATH+self.name+".bim"))):
+ if os.path.isfile(MAPPING_PATH+self.name+".bed"):
return True
return False
if check_plink_gemma():
marker_class = HumanMarkers
else:
- marker_class = Markers
+ marker_class = Markers
- self.markers = marker_class(self.name)
+ if self.genofile:
+ self.markers = marker_class(self.genofile[:-5])
+ else:
+ self.markers = marker_class(self.name)
def get_f1_parent_strains(self):
try:
@@ -344,30 +349,32 @@ class DatasetGroup(object):
if maternal and paternal:
self.parlist = [maternal, paternal]
+ def get_genofiles(self):
+ jsonfile = "%s/%s.json" % (webqtlConfig.GENODIR, self.name)
+ try:
+ f = open(jsonfile)
+ except:
+ return None
+ jsondata = json.load(f)
+ return jsondata['genofile']
+
def get_samplelist(self):
result = None
- key = "samplelist:v2:" + self.name
+ key = "samplelist:v3:" + self.name
if USE_REDIS:
result = Redis.get(key)
if result is not None:
- #logger.debug("Sample List Cache hit!!!")
- #logger.debug("Before unjsonifying {}: {}".format(type(result), result))
self.samplelist = json.loads(result)
- #logger.debug(" type: ", type(self.samplelist))
- #logger.debug(" self.samplelist: ", self.samplelist)
else:
logger.debug("Cache not hit")
genotype_fn = locate_ignore_error(self.name+".geno",'genotype')
- mapping_fn = locate_ignore_error(self.name+".fam",'mapping')
- if mapping_fn:
- self.samplelist = get_group_samplelists.get_samplelist("plink", mapping_fn)
- elif genotype_fn:
+ if genotype_fn:
self.samplelist = get_group_samplelists.get_samplelist("geno", genotype_fn)
else:
self.samplelist = None
- logger.debug("Sample list: ",self.samplelist)
+
if USE_REDIS:
Redis.set(key, json.dumps(self.samplelist))
Redis.expire(key, 60*5)
@@ -378,19 +385,27 @@ class DatasetGroup(object):
[result.extend(l) for l in lists if l]
return result
- def read_genotype_file(self):
+ def read_genotype_file(self, use_reaper=False):
'''Read genotype from .geno file instead of database'''
#genotype_1 is Dataset Object without parents and f1
#genotype_2 is Dataset Object with parents and f1 (not for intercross)
- genotype_1 = reaper.Dataset()
+ #genotype_1 = reaper.Dataset()
# reaper barfs on unicode filenames, so here we ensure it's a string
if self.genofile:
- full_filename = str(locate(self.genofile, 'genotype'))
+ if "RData" in self.genofile: #ZS: This is a temporary fix; I need to change the way the JSON files that point to multiple genotype files are structured to point to other file types like RData
+ full_filename = str(locate(self.genofile.split(".")[0] + ".geno", 'genotype'))
+ else:
+ full_filename = str(locate(self.genofile, 'genotype'))
else:
full_filename = str(locate(self.name + '.geno', 'genotype'))
- genotype_1.read(full_filename)
+
+ if use_reaper:
+ genotype_1 = reaper.Dataset()
+ genotype_1.read(full_filename)
+ else:
+ genotype_1 = gen_geno_ob.genotype(full_filename)
if genotype_1.type == "group" and self.parlist:
genotype_2 = genotype_1.add(Mat=self.parlist[0], Pat=self.parlist[1]) #, F1=_f1)
@@ -419,13 +434,16 @@ def datasets(group_name, this_group = None):
FROM PublishFreeze,InbredSet
WHERE PublishFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
- and PublishFreeze.public > %s)
+ and PublishFreeze.public > %s
+ and PublishFreeze.confidentiality < 1
+ ORDER BY PublishFreeze.Id ASC)
UNION
(SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
FROM GenoFreeze, InbredSet
WHERE GenoFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name = '%s'
- and GenoFreeze.public > %s)
+ and GenoFreeze.public > %s
+ and GenoFreeze.confidentiality < 1)
UNION
(SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
@@ -434,27 +452,34 @@ def datasets(group_name, this_group = None):
and ProbeFreeze.InbredSetId = InbredSet.Id
and InbredSet.Name like %s
and ProbeSetFreeze.public > %s
- ORDER BY Tissue.Name, ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId)
+ and ProbeSetFreeze.confidentiality < 1
+ ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
''' % (group_name, webqtlConfig.PUBLICTHRESH,
group_name, webqtlConfig.PUBLICTHRESH,
"'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
- #for tissue_name, dataset in itertools.groupby(the_results, itemgetter(0)):
- for dataset_item in the_results:
+ sorted_results = sorted(the_results, key=lambda kv: kv[0])
+
+ pheno_inserted = False #ZS: This is kind of awkward, but need to ensure Phenotypes show up before Genotypes in dropdown
+ geno_inserted = False
+ for dataset_item in sorted_results:
tissue_name = dataset_item[0]
dataset = dataset_item[1]
dataset_short = dataset_item[2]
if tissue_name in ['#PublishFreeze', '#GenoFreeze']:
- dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ if tissue_name == '#PublishFreeze' and (dataset_short == group_name + 'Publish'):
+ dataset_menu.insert(0, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ pheno_inserted = True
+ elif pheno_inserted and tissue_name == '#GenoFreeze':
+ dataset_menu.insert(1, dict(tissue=None, datasets=[(dataset, dataset_short)]))
+ geno_inserted = True
+ else:
+ dataset_menu.append(dict(tissue=None, datasets=[(dataset, dataset_short)]))
else:
- dataset_sub_menu = [item[1:] for item in dataset]
-
tissue_already_exists = False
- tissue_position = None
for i, tissue_dict in enumerate(dataset_menu):
if tissue_dict['tissue'] == tissue_name:
tissue_already_exists = True
- tissue_position = i
break
if tissue_already_exists:
@@ -481,7 +506,7 @@ class DataSet(object):
"""
- def __init__(self, name, get_samplelist = True):
+ def __init__(self, name, get_samplelist = True, group_name = None):
assert name, "Need a name"
self.name = name
@@ -493,11 +518,13 @@ class DataSet(object):
self.setup()
- self.check_confidentiality()
-
- self.retrieve_other_names()
-
- self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
+ if self.type == "Temp": #Need to supply group name as input if temp trait
+ self.group = DatasetGroup(self, name=group_name) # sets self.group and self.group_id and gets genotype
+ else:
+ self.check_confidentiality()
+ self.retrieve_other_names()
+ self.group = DatasetGroup(self) # sets self.group and self.group_id and gets genotype
+ self.accession_id = self.get_accession_id()
if get_samplelist == True:
self.group.get_samplelist()
self.species = species.TheSpecies(self)
@@ -512,6 +539,31 @@ class DataSet(object):
def riset():
Weve_Renamed_This_As_Group
+ def get_accession_id(self):
+ if self.type == "Publish":
+ results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, PublishFreeze, InbredSet where
+ InbredSet.Name = %s and
+ PublishFreeze.InbredSetId = InbredSet.Id and
+ InfoFiles.InfoPageName = PublishFreeze.Name and
+ PublishFreeze.public > 0 and
+ PublishFreeze.confidentiality < 1 order by
+ PublishFreeze.CreateTime desc""", (self.group.name)).fetchone()
+ elif self.type == "Geno":
+ results = g.db.execute("""select InfoFiles.GN_AccesionId from InfoFiles, GenoFreeze, InbredSet where
+ InbredSet.Name = %s and
+ GenoFreeze.InbredSetId = InbredSet.Id and
+ InfoFiles.InfoPageName = GenoFreeze.ShortName and
+ GenoFreeze.public > 0 and
+ GenoFreeze.confidentiality < 1 order by
+ GenoFreeze.CreateTime desc""", (self.group.name)).fetchone()
+ else:
+ results = None
+
+ if results != None:
+ return str(results[0])
+ else:
+ return "None"
+
def retrieve_other_names(self):
"""This method fetches the the dataset names in search_result.
@@ -658,6 +710,7 @@ class PhenotypeDataSet(DataSet):
'Phenotype.Pre_publication_description',
'Phenotype.Pre_publication_abbreviation',
'Phenotype.Post_publication_abbreviation',
+ 'PublishXRef.mean',
'Phenotype.Lab_code',
'Publication.PubMed_ID',
'Publication.Abstract',
@@ -666,13 +719,14 @@ class PhenotypeDataSet(DataSet):
'PublishXRef.Id']
# Figure out what display_fields is
- self.display_fields = ['name',
+ self.display_fields = ['name', 'group_code',
'pubmed_id',
'pre_publication_description',
'post_publication_description',
'original_description',
'pre_publication_abbreviation',
'post_publication_abbreviation',
+ 'mean',
'lab_code',
'submitter', 'owner',
'authorized_users',
@@ -708,20 +762,6 @@ class PhenotypeDataSet(DataSet):
# (Urgently?) Need to write this
pass
- def get_trait_list(self):
- query = """
- select PublishXRef.Id
- from PublishXRef, PublishFreeze
- where PublishFreeze.InbredSetId=PublishXRef.InbredSetId
- and PublishFreeze.Id = {}
- """.format(escape(str(self.id)))
- logger.sql(query)
- results = g.db.execute(query).fetchall()
- trait_data = {}
- for trait in results:
- trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
- return trait_data
-
def get_trait_info(self, trait_list, species = ''):
for this_trait in trait_list:
@@ -735,7 +775,7 @@ class PhenotypeDataSet(DataSet):
#of the post-publication description
if this_trait.confidential:
this_trait.description_display = ""
- continue # for now
+ continue # for now, because no authorization features
if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
privilege=self.privilege,
@@ -759,9 +799,7 @@ class PhenotypeDataSet(DataSet):
#LRS and its location
this_trait.LRS_score_repr = "N/A"
- this_trait.LRS_score_value = 0
this_trait.LRS_location_repr = "N/A"
- this_trait.LRS_location_value = 1000000
if this_trait.lrs:
query = """
@@ -778,17 +816,7 @@ class PhenotypeDataSet(DataSet):
LRS_Chr = result[0]
LRS_Mb = result[1]
- #XZ: LRS_location_value is used for sorting
- try:
- LRS_location_value = int(LRS_Chr)*1000 + float(LRS_Mb)
- except:
- if LRS_Chr.upper() == 'X':
- LRS_location_value = 20*1000 + float(LRS_Mb)
- else:
- LRS_location_value = ord(str(LRS_chr).upper()[0])*1000 + float(LRS_Mb)
-
this_trait.LRS_score_repr = LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_score_value = LRS_score_value = this_trait.lrs
this_trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (LRS_Chr, float(LRS_Mb))
def retrieve_sample_data(self, trait):
@@ -850,45 +878,18 @@ class GenotypeDataSet(DataSet):
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
- def get_trait_list(self):
- query = """
- select Geno.Name
- from Geno, GenoXRef
- where GenoXRef.GenoId = Geno.Id
- and GenoFreezeId = {}
- """.format(escape(str(self.id)))
- logger.sql(query)
- results = g.db.execute(query).fetchall()
- trait_data = {}
- for trait in results:
- trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
- return trait_data
-
def get_trait_info(self, trait_list, species=None):
for this_trait in trait_list:
if not this_trait.haveinfo:
this_trait.retrieveInfo()
- #XZ: trait_location_value is used for sorting
- trait_location_repr = 'N/A'
- trait_location_value = 1000000
-
if this_trait.chr and this_trait.mb:
- try:
- trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
- except:
- if this_trait.chr.upper() == 'X':
- trait_location_value = 20*1000 + this_trait.mb
- else:
- trait_location_value = ord(str(this_trait.chr).upper()[0])*1000 + this_trait.mb
-
this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb) )
- this_trait.location_value = trait_location_value
def retrieve_sample_data(self, trait):
query = """
SELECT
- Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Sample.Name2
+ Strain.Name, GenoData.value, GenoSE.error, GenoData.Id, Strain.Name2
FROM
(GenoData, GenoFreeze, Strain, Geno, GenoXRef)
left join GenoSE on
@@ -940,6 +941,7 @@ class MrnaAssayDataSet(DataSet):
'blatseq', 'targetseq',
'chipid', 'comments',
'strand_probe', 'strand_gene',
+ 'proteinid', 'uniprotid',
'probe_set_target_region',
'probe_set_specificity',
'probe_set_blat_score',
@@ -978,20 +980,6 @@ class MrnaAssayDataSet(DataSet):
def check_confidentiality(self):
return geno_mrna_confidentiality(self)
- def get_trait_list_1(self):
- query = """
- select ProbeSet.Name
- from ProbeSet, ProbeSetXRef
- where ProbeSetXRef.ProbeSetId = ProbeSet.Id
- and ProbeSetFreezeId = {}
- """.format(escape(str(self.id)))
- logger.sql(query)
- results = g.db.execute(query).fetchall()
- trait_data = {}
- for trait in results:
- trait_data[trait[0]] = self.retrieve_sample_data(trait[0])
- return trait_data
-
def get_trait_info(self, trait_list=None, species=''):
# Note: setting trait_list to [] is probably not a great idea.
@@ -1023,27 +1011,8 @@ class MrnaAssayDataSet(DataSet):
# Save it for the jinja2 template
this_trait.description_display = description_display
- #XZ: trait_location_value is used for sorting
- trait_location_repr = 'N/A'
- trait_location_value = 1000000
-
if this_trait.chr and this_trait.mb:
- #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
- #This is so we can convert the location to a number used for sorting
- trait_location_value = self.convert_location_to_value(this_trait.chr, this_trait.mb)
- #try:
- # trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
- #except ValueError:
- # if this_trait.chr.upper() == 'X':
- # trait_location_value = 20*1000 + this_trait.mb
- # else:
- # trait_location_value = (ord(str(this_trait.chr).upper()[0])*1000 +
- # this_trait.mb)
-
- #ZS: Put this in function currently called "convert_location_to_value"
- this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr,
- float(this_trait.mb))
- this_trait.location_value = trait_location_value
+ this_trait.location_repr = 'Chr%s: %.6f' % (this_trait.chr, float(this_trait.mb))
#Get mean expression value
query = (
@@ -1065,9 +1034,7 @@ class MrnaAssayDataSet(DataSet):
#LRS and its location
this_trait.LRS_score_repr = 'N/A'
- this_trait.LRS_score_value = 0
this_trait.LRS_location_repr = 'N/A'
- this_trait.LRS_location_value = 1000000
#Max LRS and its Locus location
if this_trait.lrs and this_trait.locus:
@@ -1082,40 +1049,10 @@ class MrnaAssayDataSet(DataSet):
if result:
lrs_chr, lrs_mb = result
- #XZ: LRS_location_value is used for sorting
- lrs_location_value = self.convert_location_to_value(lrs_chr, lrs_mb)
this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs
- this_trait.LRS_score_value = this_trait.lrs
this_trait.LRS_location_repr = 'Chr%s: %.6f' % (lrs_chr, float(lrs_mb))
-
- def convert_location_to_value(self, chromosome, mb):
- try:
- location_value = int(chromosome)*1000 + float(mb)
- except ValueError:
- if chromosome.upper() == 'X':
- location_value = 20*1000 + float(mb)
- else:
- location_value = (ord(str(chromosome).upper()[0])*1000 +
- float(mb))
-
- return location_value
-
- def get_sequence(self):
- query = """
- SELECT
- ProbeSet.BlatSeq
- FROM
- ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE
- ProbeSet.Id=ProbeSetXRef.ProbeSetId and
- ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
- ProbeSet.Name = %s
- ProbeSetFreeze.Name = %s
- """ % (escape(self.name), escape(self.dataset.name))
- logger.sql(query)
- results = g.db.execute(query).fetchone()
- return results[0]
+ return trait_list
def retrieve_sample_data(self, trait):
query = """
@@ -1139,7 +1076,6 @@ class MrnaAssayDataSet(DataSet):
#logger.debug("RETRIEVED RESULTS HERE:", results)
return results
-
def retrieve_genes(self, column_name):
query = """
select ProbeSet.Name, ProbeSet.%s
@@ -1156,6 +1092,8 @@ class MrnaAssayDataSet(DataSet):
class TempDataSet(DataSet):
'''Temporary user-generated data set'''
+ DS_NAME_MAP['Temp'] = 'TempDataSet'
+
def setup(self):
self.search_fields = ['name',
'description']
@@ -1191,19 +1129,6 @@ class TempDataSet(DataSet):
desc = self.handle_pca(desc)
return desc
- def get_group(self):
- query = """
- SELECT
- InbredSet.Name, InbredSet.Id
- FROM
- InbredSet, Temp
- WHERE
- Temp.InbredSetId = InbredSet.Id AND
- Temp.Name = "%s"
- """ % self.name
- logger.sql(query)
- self.group, self.group_id = g.db.execute(query).fetchone()
-
def retrieve_sample_data(self, trait):
query = """
SELECT
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index eb836e6c..6fec5dcd 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -18,21 +18,11 @@ class MrnaAssayTissueData(object):
def __init__(self, gene_symbols=None):
self.gene_symbols = gene_symbols
- self.have_data = False
if self.gene_symbols == None:
self.gene_symbols = []
- #print("self.gene_symbols:", self.gene_symbols)
-
self.data = collections.defaultdict(Bunch)
- #self.gene_id_dict ={}
- #self.data_id_dict = {}
- #self.chr_dict = {}
- #self.mb_dict = {}
- #self.desc_dict = {}
- #self.probe_target_desc_dict = {}
-
query = '''select t.Symbol, t.GeneId, t.DataId, t.Chr, t.Mb, t.description, t.Probe_Target_Description
from (
select Symbol, max(Mean) as maxmean
@@ -52,7 +42,6 @@ class MrnaAssayTissueData(object):
in_clause = db_tools.create_in_clause(gene_symbols)
#ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
-
query += ''' Symbol in {} group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
and t.Mean = x.maxmean;
@@ -67,9 +56,7 @@ class MrnaAssayTissueData(object):
for result in results:
symbol = result[0]
- #if symbol.lower() in [gene_symbol.lower() for gene_symbol in gene_symbols]:
if symbol.lower() in lower_symbols:
- #gene_symbols.append(symbol)
symbol = symbol.lower()
self.data[symbol].gene_id = result.GeneId
@@ -79,8 +66,6 @@ class MrnaAssayTissueData(object):
self.data[symbol].description = result.description
self.data[symbol].probe_target_description = result.Probe_Target_Description
- print("self.data: ", pf(self.data))
-
###########################################################################
#Input: cursor, symbolList (list), dataIdDict(Dict)
#output: symbolValuepairDict (dictionary):one dictionary of Symbol and Value Pair,
@@ -107,53 +92,4 @@ class MrnaAssayTissueData(object):
else:
symbol_values_dict[result.Symbol.lower()].append(result.value)
- #for symbol in self.data:
- # data_id = self.data[symbol].data_id
- # symbol_values_dict[symbol] = self.get_tissue_values(data_id)
-
-
- return symbol_values_dict
-
-
- #def get_tissue_values(self, data_id):
- # """Gets the tissue values for a particular gene"""
- #
- # tissue_values=[]
- #
- # query = """SELECT value, id
- # FROM TissueProbeSetData
- # WHERE Id IN {}""".format(db_tools.create_in_clause(data_id))
- #
- # #try :
- # results = g.db.execute(query).fetchall()
- # for result in results:
- # tissue_values.append(result.value)
- # #symbol_values_dict[symbol] = value_list
- # #except:
- # # symbol_values_pairs[symbol] = None
- #
- # return tissue_values
-
-########################################################################################################
-#input: cursor, symbolList (list), dataIdDict(Dict): key is symbol
-#output: SymbolValuePairDict(dictionary):one dictionary of Symbol and Value Pair.
-# key is symbol, value is one list of expression values of one probeSet.
-#function: wrapper function for getSymbolValuePairDict function
-# build gene symbol list if necessary, cut it into small lists if necessary,
-# then call getSymbolValuePairDict function and merge the results.
-########################################################################################################
-
-#def get_trait_symbol_and_tissue_values(symbol_list=None):
-# tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
-#
-# #symbolList,
-# #geneIdDict,
-# #dataIdDict,
-# #ChrDict,
-# #MbDict,
-# #descDict,
-# #pTargetDescDict = getTissueProbeSetXRefInfo(
-# # GeneNameLst=GeneNameLst,TissueProbeSetFreezeId=TissueProbeSetFreezeId)
-#
-# if len(tissue_data.gene_symbols):
-# return get_symbol_values_pairs(tissue_data)
+ return symbol_values_dict \ No newline at end of file
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index ce763fc3..6d99af65 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -14,23 +14,13 @@ from utility.logger import getLogger
logger = getLogger(__name__ )
class TheSpecies(object):
- def __init__(self, dataset):
- self.dataset = dataset
- #print("self.dataset is:", pf(self.dataset.__dict__))
- self.chromosomes = Chromosomes(self.dataset)
- self.genome_mb_length = self.chromosomes.get_genome_mb_length()
-
- #@property
- #def chromosomes(self):
- # chromosomes = [("All", -1)]
- #
- # for counter, genotype in enumerate(self.dataset.group.genotype):
- # if len(genotype) > 1:
- # chromosomes.append((genotype.name, counter))
- #
- # print("chromosomes is: ", pf(chromosomes))
- #
- # return chromosomes
+ def __init__(self, dataset=None, species_name=None):
+ if species_name != None:
+ self.name = species_name
+ self.chromosomes = Chromosomes(species=self.name)
+ else:
+ self.dataset = dataset
+ self.chromosomes = Chromosomes(dataset=self.dataset)
class IndChromosome(object):
def __init__(self, name, length):
@@ -42,17 +32,22 @@ class IndChromosome(object):
"""Chromosome length in megabases"""
return self.length / 1000000
- def set_cm_length(self, genofile_chr):
- self.cm_length = genofile_chr[-1].cM - genofile_chr[0].cM
-
-
class Chromosomes(object):
- def __init__(self, dataset):
- self.dataset = dataset
+ def __init__(self, dataset=None, species=None):
self.chromosomes = collections.OrderedDict()
+ if species != None:
+ query = """
+ Select
+ Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, Species
+ where
+ Chr_Length.SpeciesId = Species.SpeciesId AND
+ Species.Name = '%s'
+ Order by OrderId
+ """ % species.capitalize()
+ else:
+ self.dataset = dataset
-
- query = """
+ query = """
Select
Chr_Length.Name, Chr_Length.OrderId, Length from Chr_Length, InbredSet
where
@@ -64,64 +59,4 @@ class Chromosomes(object):
results = g.db.execute(query).fetchall()
for item in results:
- self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
-
- self.set_mb_graph_interval()
- #self.get_cm_length_list()
-
-
- def set_mb_graph_interval(self):
- """Empirical megabase interval"""
-
- if self.chromosomes:
- self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
- else:
- self.mb_graph_interval = 1
-
- #if self.chromosomes:
- #assert self.chromosomes, "Have to add some code back in apparently to set it to 1"
- #self.mb_graph_interval = self.get_genome_mb_length()/(len(self.chromosomes)*12)
- #else:
- #self.mb_graph_interval = 1
-
-
- def get_genome_mb_length(self):
- """Gets the sum of each chromosome's length in megabases"""
-
- return sum([ind_chromosome.mb_length for ind_chromosome in self.chromosomes.values()])
-
-
- def get_genome_cm_length(self):
- """Gets the sum of each chromosome's length in centimorgans"""
-
- return sum([ind_chromosome.cm_length for ind_chromosome in self.chromosomes.values()])
-
- def get_cm_length_list(self):
- """Chromosome length in centimorgans
-
- Calculates the length in centimorgans by subtracting the centimorgan position
- of the last marker in a chromosome by the position of the first marker
-
- """
-
- self.dataset.group.read_genotype_file()
-
- self.cm_length_list = []
-
- for chromosome in self.dataset.group.genotype:
- self.cm_length_list.append(chromosome[-1].cM - chromosome[0].cM)
-
- print("self.cm_length_list:", pf(self.cm_length_list))
-
- assert len(self.cm_length_list) == len(self.chromosomes), "Uh-oh lengths should be equal!"
- for counter, chromosome in enumerate(self.chromosomes.values()):
- chromosome.cm_length = self.cm_length_list[counter]
- #self.chromosomes[counter].cm_length = item
-
- for key, value in self.chromosomes.items():
- print("bread - %s: %s" % (key, pf(vars(value))))
-
-
-# Testing
-#if __name__ == '__main__':
-# foo = dict(bar=dict(length))
+ self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length) \ No newline at end of file
diff --git a/wqflask/base/template.py b/wqflask/base/template.py
deleted file mode 100644
index aa8f90dc..00000000
--- a/wqflask/base/template.py
+++ /dev/null
@@ -1,123 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-template = """
-<?XML VERSION="1.0" ENCODING="UTF-8">
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
-<HTML>
-<HEAD>
-<TITLE>%s</TITLE>
-
-<META http-equiv=Content-Type content="text/html; charset=iso-8859-1">
-<META NAME="keywords" CONTENT="genetics, bioinformatics, genome, phenome, gene expression, complex trait analysis, gene mapping, SNP, quantitative trait locus QTL, expression eQTL, WebQTL, Traitnet, Traitnetwork, personalized medicine">
-<META NAME="description" CONTENT ="GeneNetwork is a free scientific web resource used to study relationships between differences in genes, environmental factors, phenotypes, and disease risk." >
-<META NAME="author" CONTENT ="GeneNetwork developers" >
-<META NAME="geo.placename" CONTENT ="Memphis, TN" >
-<META NAME="geo.region" CONTENT="US-TN">
-%s
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/general.css'>
-<LINK REL="stylesheet" TYPE="text/css" HREF='/css/menu.css'>
-<link rel="stylesheet" media="all" type="text/css" href="/css/tabbed_pages.css" />
-<LINK REL="apple-touch-icon" href="/images/ipad_icon3.png" />
-<link type="text/css" href='/css/custom-theme/jquery-ui-1.8.12.custom.css' rel='Stylesheet' />
-<link type="text/css" href='/css/tab_style.css' rel='Stylesheet' />
-
-<script type="text/javascript" src="/javascript/jquery-1.5.2.min.js"></script>
-<SCRIPT SRC="/javascript/webqtl.js"></SCRIPT>
-<SCRIPT SRC="/javascript/dhtml.js"></SCRIPT>
-<SCRIPT SRC="/javascript/tablesorter.js"></SCRIPT>
-<SCRIPT SRC="/javascript/jqueryFunction.js"></SCRIPT>
-<script src="/javascript/tabbed_pages.js" type="text/javascript"></script>
-<script src="/javascript/jquery-ui-1.8.12.custom.min.js" type="text/javascript"></script>
-%s
-
-<script type="text/javascript">
- var _gaq = _gaq || [];
- _gaq.push(['_setAccount', 'UA-3782271-1']);
- _gaq.push(['_trackPageview']);
- (function() {
- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
- })();
-</script>
-</HEAD>
-<BODY bottommargin="2" leftmargin="2" rightmargin="2" topmargin="2" text=#000000 bgColor=#ffffff %s>
-%s
-<TABLE cellSpacing=5 cellPadding=4 width="100%%" border=0>
- <TBODY>
- <!-- Start of header -->
- <TR>
- %s
- </TR>
- <!-- End of header -->
-
- <!-- Start of body -->
- <TR>
- <TD bgColor=#eeeeee class="solidBorder">
- <Table width= "100%%" cellSpacing=0 cellPadding=5>
- <TR>
- %s
- </TR>
- </TABLE>
- </TD>
- </TR>
- <!-- End of body -->
-
- <!-- Start of footer -->
- <TR>
- <TD align=center bgColor=#ddddff class="solidBorder">
- <TABLE width="90%%">%s</table>
- </td>
- </TR>
- <!-- End of footer -->
-</TABLE>
-
-<!-- menu script itself. you should not modify this file -->
-<script language="JavaScript" src="/javascript/menu_new.js"></script>
-<!-- items structure. menu hierarchy and links are stored there -->
-<script language="JavaScript" src="/javascript/menu_items.js"></script>
-<!-- files with geometry and styles structures -->
-<script language="JavaScript" src="/javascript/menu_tpl.js"></script>
-<script language="JavaScript">
- <!--//
- // Note where menu initialization block is located in HTML document.
- // Don't try to position menu locating menu initialization block in
- // some table cell or other HTML element. Always put it before </body>
- // each menu gets two parameters (see demo files)
- // 1. items structure
- // 2. geometry structure
- new menu (MENU_ITEMS, MENU_POS);
- // make sure files containing definitions for these variables are linked to the document
- // if you got some javascript error like "MENU_POS is not defined", then you've made syntax
- // error in menu_tpl.js file or that file isn't linked properly.
-
- // also take a look at stylesheets loaded in header in order to set styles
- //-->
-</script>
-</BODY>
-</HTML>
-"""
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index bf87e879..5525472e 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -3,14 +3,17 @@ from __future__ import absolute_import, division, print_function
import string
import resource
import codecs
+import requests
-from htmlgen import HTMLgen2 as HT
+import redis
+Redis = redis.StrictRedis()
from base import webqtlConfig
from base.webqtlCaseData import webqtlCaseData
from base.data_set import create_dataset
from db import webqtlDatabaseFunction
from utility import webqtlUtil
+from utility import hmac
from wqflask import app
@@ -18,17 +21,11 @@ import simplejson as json
from MySQLdb import escape_string as escape
from pprint import pformat as pf
-from flask import Flask, g, request
+from flask import Flask, g, request, url_for
from utility.logger import getLogger
logger = getLogger(__name__ )
-from wqflask import user_manager
-
-def print_mem(stage=""):
- mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss
- print("{}: {}".format(stage, mem/1024))
-
class GeneralTrait(object):
"""
Trait class defines a trait in webqtl, can be either Microarray,
@@ -39,13 +36,15 @@ class GeneralTrait(object):
def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
# xor assertion
assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
+ self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
if kw.get('dataset_name'):
- self.dataset = create_dataset(kw.get('dataset_name'))
- #print(" in GeneralTrait created dataset:", self.dataset)
+ if kw.get('dataset_name') == "Temp":
+ temp_group = self.name.split("_")[2]
+ self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+ else:
+ self.dataset = create_dataset(kw.get('dataset_name'))
else:
self.dataset = kw.get('dataset')
- self.name = kw.get('name') # Trait ID, ProbeSet ID, Published ID, etc.
- #print("THE NAME IS:", self.name)
self.cellid = kw.get('cellid')
self.identification = kw.get('identification', 'un-named trait')
self.haveinfo = kw.get('haveinfo', False)
@@ -61,6 +60,10 @@ class GeneralTrait(object):
self.num_overlap = None
self.strand_probe = None
self.symbol = None
+ self.display_name = self.name
+
+ self.LRS_score_repr = "N/A"
+ self.LRS_location_repr = "N/A"
if kw.get('fullname'):
name2 = value.split("::")
@@ -72,94 +75,11 @@ class GeneralTrait(object):
# Todo: These two lines are necessary most of the time, but perhaps not all of the time
# So we could add a simple if statement to short-circuit this if necessary
- self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
+ if self.dataset.type != "Temp":
+ self = retrieve_trait_info(self, self.dataset, get_qtl_info=get_qtl_info)
if get_sample_info != False:
self = retrieve_sample_data(self, self.dataset)
-
- def get_name(self):
- stringy = ""
- if self.dataset and self.name:
- stringy = "%s::%s" % (self.dataset, self.name)
- if self.cellid:
- stringy += "::" + self.cellid
- else:
- stringy = self.description
- return stringy
-
-
- def get_given_name(self):
- """
- when user enter a trait or GN generate a trait, user want show the name
- not the name that generated by GN randomly, the two follow function are
- used to give the real name and the database. displayName() will show the
- database also, getGivenName() just show the name.
- For other trait, displayName() as same as getName(), getGivenName() as
- same as self.name
-
- Hongqiang 11/29/07
-
- """
- stringy = self.name
- if self.dataset and self.name:
- desc = self.dataset.get_desc()
- if desc:
- #desc = self.handle_pca(desc)
- stringy = desc
- return stringy
-
-
- def display_name(self):
- stringy = ""
- if self.dataset and self.name:
- desc = self.dataset.get_desc()
- #desc = self.handle_pca(desc)
- if desc:
- #desc = self.handle_pca(desc)
- #stringy = desc
- #if desc.__contains__('PCA'):
- # desc = desc[desc.rindex(':')+1:].strip()
- #else:
- # desc = desc[:desc.index('entered')].strip()
- #desc = self.handle_pca(desc)
- stringy = "%s::%s" % (self.dataset, desc)
- else:
- stringy = "%s::%s" % (self.dataset, self.name)
- if self.cellid:
- stringy += "::" + self.cellid
- else:
- stringy = self.description
-
- return stringy
-
-
- #def __str__(self):
- # #return "%s %s" % (self.getName(), self.group)
- # return self.getName()
- #__str__ = getName
- #__repr__ = __str__
-
- def export_data(self, samplelist, the_type="val"):
- """
- export data according to samplelist
- mostly used in calculating correlation
-
- """
- result = []
- for sample in samplelist:
- if self.data.has_key(sample):
- if the_type=='val':
- result.append(self.data[sample].val)
- elif the_type=='var':
- result.append(self.data[sample].var)
- elif the_type=='N':
- result.append(self.data[sample].N)
- else:
- raise KeyError, `the_type`+' the_type is incorrect.'
- else:
- result.append(None)
- return result
-
def export_informative(self, include_variance=0):
"""
export informative sample
@@ -179,19 +99,6 @@ class GeneralTrait(object):
sample_aliases.append(sample_data.name2)
return samples, vals, the_vars, sample_aliases
-
- @property
- def name_header_fmt(self):
- '''Return a human-readable name for use in page header'''
- if self.dataset.type == 'ProbeSet':
- return self.symbol
- elif self.dataset.type == 'Geno':
- return self.name
- elif self.dataset.type == 'Publish':
- return self.post_publication_abbreviation
- else:
- return "unnamed"
-
@property
def description_fmt(self):
'''Return a text formated description'''
@@ -200,6 +107,8 @@ class GeneralTrait(object):
formatted = self.description
if self.probe_target_description:
formatted += "; " + self.probe_target_description
+ else:
+ formatted = "Not available"
elif self.dataset.type == 'Publish':
if self.confidential:
formatted = self.pre_publication_description
@@ -212,11 +121,36 @@ class GeneralTrait(object):
@property
def alias_fmt(self):
'''Return a text formatted alias'''
+
+ alias = 'Not available'
if self.alias:
alias = string.replace(self.alias, ";", " ")
alias = string.join(string.split(alias), ", ")
- else:
- alias = 'Not available'
+
+ return alias
+
+ @property
+ def wikidata_alias_fmt(self):
+ '''Return a text formatted alias'''
+
+ alias = 'Not available'
+ if self.symbol:
+ human_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.upper())
+ mouse_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.capitalize())
+ other_response = requests.get("http://gn2.genenetwork.org/gn3/gene/aliases/" + self.symbol.lower())
+
+ if human_response and mouse_response and other_response:
+ alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)
+
+ filtered_aliases = []
+ seen = set()
+ for item in alias_list:
+ if item in seen:
+ continue
+ else:
+ filtered_aliases.append(item)
+ seen.add(item)
+ alias = "; ".join(filtered_aliases)
return alias
@@ -244,60 +178,33 @@ class GeneralTrait(object):
fmt += (' on the minus strand ')
return fmt
-
-# In ProbeSet, there are maybe several annotations match one sequence
-# so we need use sequence(BlatSeq) as the identification, when we update
-# one annotation, we update the others who match the sequence also.
-#
-# Hongqiang Li, 3/3/2008
-def getSequence(trait, dataset_name):
- dataset = create_dataset(dataset_name)
-
- if dataset.type == 'ProbeSet':
- results = g.db.execute('''
- SELECT
- ProbeSet.BlatSeq
- FROM
- ProbeSet, ProbeSetFreeze, ProbeSetXRef
- WHERE
- ProbeSet.Id=ProbeSetXRef.ProbeSetId and
- ProbeSetFreeze.Id = ProbeSetXRef.ProbSetFreezeId and
- ProbeSet.Name = %s
- ProbeSetFreeze.Name = %s
- ''', trait.name, dataset.name).fetchone()
-
- return results[0]
def retrieve_sample_data(trait, dataset, samplelist=None):
if samplelist == None:
samplelist = []
- results = dataset.retrieve_sample_data(trait.name)
+ if dataset.type == "Temp":
+ results = Redis.get(trait.name).split()
+ else:
+ results = dataset.retrieve_sample_data(trait.name)
# Todo: is this necessary? If not remove
trait.data.clear()
- all_samples_ordered = dataset.group.all_samples_ordered()
-
if results:
- for item in results:
- name, value, variance, num_cases, name2 = item
- if not samplelist or (samplelist and name in samplelist):
- trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
-
- return trait
-
-def convert_location_to_value(chromosome, mb):
- try:
- location_value = int(chromosome)*1000 + float(mb)
- except ValueError:
- if chromosome.upper() == 'X':
- location_value = 20*1000 + float(mb)
+ if dataset.type == "Temp":
+ all_samples_ordered = dataset.group.all_samples_ordered()
+ for i, item in enumerate(results):
+ try:
+ trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+ except:
+ pass
else:
- location_value = (ord(str(chromosome).upper()[0])*1000 +
- float(mb))
-
- return location_value
+ for item in results:
+ name, value, variance, num_cases, name2 = item
+ if not samplelist or (samplelist and name in samplelist):
+ trait.data[name] = webqtlCaseData(*item) #name, value, variance, num_cases)
+ return trait
@app.route("/trait/get_sample_data")
def get_sample_data():
@@ -307,25 +214,37 @@ def get_sample_data():
trait_ob = GeneralTrait(name=trait, dataset_name=dataset)
- return json.dumps([trait, {key: value.value for key, value in trait_ob.data.iteritems() }])
-
- #jsonable_sample_data = {}
- #for sample in trait_ob.data.iteritems():
- # jsonable_sample_data[sample] = trait_ob.data[sample].value
- #
- #return jsonable_sample_data
+ trait_dict = {}
+ trait_dict['name'] = trait
+ trait_dict['db'] = dataset
+ trait_dict['type'] = trait_ob.dataset.type
+ trait_dict['group'] = trait_ob.dataset.group.name
+ trait_dict['tissue'] = trait_ob.dataset.tissue
+ trait_dict['species'] = trait_ob.dataset.group.species
+ trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+ trait_dict['description'] = trait_ob.description_display
+ if trait_ob.dataset.type == "ProbeSet":
+ trait_dict['symbol'] = trait_ob.symbol
+ trait_dict['location'] = trait_ob.location_repr
+ elif trait_ob.dataset.type == "Publish":
+ if trait_ob.pubmed_id:
+ trait_dict['pubmed_link'] = trait_ob.pubmed_link
+ trait_dict['pubmed_text'] = trait_ob.pubmed_text
+
+ return json.dumps([trait_dict, {key: value.value for key, value in trait_ob.data.iteritems() }])
-def jsonable(trait, dataset_name):
+def jsonable(trait):
"""Return a dict suitable for using as json
Actual turning into json doesn't happen here though"""
- dataset = create_dataset(dataset_name)
+ dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
if dataset.type == "ProbeSet":
return dict(name=trait.name,
symbol=trait.symbol,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
description=trait.description_display,
mean=trait.mean,
location=trait.location_repr,
@@ -337,7 +256,9 @@ def jsonable(trait, dataset_name):
if trait.pubmed_id:
return dict(name=trait.name,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
description=trait.description_display,
+ abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
pubmed_link=trait.pubmed_link,
@@ -348,7 +269,9 @@ def jsonable(trait, dataset_name):
else:
return dict(name=trait.name,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
description=trait.description_display,
+ abbreviation=trait.abbreviation,
authors=trait.authors,
pubmed_text=trait.pubmed_text,
lrs_score=trait.LRS_score_repr,
@@ -358,6 +281,7 @@ def jsonable(trait, dataset_name):
elif dataset.type == "Geno":
return dict(name=trait.name,
dataset=dataset.name,
+ dataset_name = dataset.shortname,
location=trait.location_repr
)
else:
@@ -379,7 +303,7 @@ def jsonable_table_row(trait, dataset_name, index):
additive = "N/A"
else:
additive = "%.3f" % round(float(trait.additive), 2)
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.symbol,
@@ -395,7 +319,7 @@ def jsonable_table_row(trait, dataset_name, index):
else:
additive = "%.2f" % round(float(trait.additive), 2)
if trait.pubmed_id:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.description_display,
@@ -405,7 +329,7 @@ def jsonable_table_row(trait, dataset_name, index):
trait.LRS_location_repr,
additive]
else:
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.description_display,
@@ -415,7 +339,7 @@ def jsonable_table_row(trait, dataset_name, index):
trait.LRS_location_repr,
additive]
elif dataset.type == "Geno":
- return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + user_manager.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
+ return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
index,
'<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
trait.location_repr]
@@ -428,21 +352,22 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if dataset.type == 'Publish':
query = """
SELECT
- PublishXRef.Id, Publication.PubMed_ID,
+ PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
- Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+ Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
Publication.Authors, Publication.Title, Publication.Abstract,
Publication.Journal, Publication.Volume, Publication.Pages,
Publication.Month, Publication.Year, PublishXRef.Sequence,
Phenotype.Units, PublishXRef.comments
FROM
- PublishXRef, Publication, Phenotype, PublishFreeze
+ PublishXRef, Publication, Phenotype, PublishFreeze, InbredSet
WHERE
PublishXRef.Id = %s AND
Phenotype.Id = PublishXRef.PhenotypeId AND
Publication.Id = PublishXRef.PublicationId AND
PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND
+ PublishXRef.InbredSetId = InbredSet.Id AND
PublishFreeze.Id = %s
""" % (trait.name, dataset.id)
@@ -492,17 +417,25 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait_info = g.db.execute(query,
(string.join(dataset.display_fields,','),
dataset.type, trait.name)).fetchone()
+
if trait_info:
trait.haveinfo = True
#XZ: assign SQL query result to trait attributes.
for i, field in enumerate(dataset.display_fields):
holder = trait_info[i]
+ # if isinstance(trait_info[i], basestring):
+ # logger.debug("HOLDER:", holder)
+ # logger.debug("HOLDER2:", holder.decode(encoding='latin1'))
+ # holder = unicode(trait_info[i], "utf-8", "ignore")
if isinstance(trait_info[i], basestring):
- holder = unicode(trait_info[i], "utf-8", "ignore")
+ holder = holder.encode('latin1')
setattr(trait, field, holder)
if dataset.type == 'Publish':
+ if trait.group_code:
+ trait.display_name = trait.group_code + "_" + str(trait.name)
+
trait.confidential = 0
if trait.pre_publication_description and not trait.pubmed_id:
trait.confidential = 1
@@ -513,6 +446,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#phenotype traits, then display the pre-publication description instead
#of the post-publication description
if trait.confidential:
+ trait.abbreviation = trait.pre_publication_abbreviation
trait.description_display = trait.pre_publication_description
#if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(
@@ -522,11 +456,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#
# description = self.pre_publication_description
else:
+ trait.abbreviation = trait.post_publication_abbreviation
if description:
trait.description_display = description.strip()
else:
trait.description_display = ""
+ trait.abbreviation = unicode(str(trait.abbreviation).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+ trait.description_display = unicode(str(trait.description_display).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+ trait.authors = unicode(str(trait.authors).strip(codecs.BOM_UTF8), 'utf-8', errors="replace")
+
if not trait.year.isdigit():
trait.pubmed_text = "N/A"
else:
@@ -535,38 +474,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
if trait.pubmed_id:
trait.pubmed_link = webqtlConfig.PUBMEDLINK_URL % trait.pubmed_id
-
- trait.homologeneid = None
if dataset.type == 'ProbeSet' and dataset.group:
- if trait.geneid:
- #XZ, 05/26/2010: From time to time, this query get error message because some geneid values in database are not number.
- #XZ: So I have to test if geneid is number before execute the query.
- #XZ: The geneid values in database should be cleaned up.
- #try:
- # float(self.geneid)
- # geneidIsNumber = True
- #except ValueError:
- # geneidIsNumber = False
- #if geneidIsNumber:
- query = """
- SELECT
- HomologeneId
- FROM
- Homologene, Species, InbredSet
- WHERE
- Homologene.GeneId ='%s' AND
- InbredSet.Name = '%s' AND
- InbredSet.SpeciesId = Species.Id AND
- Species.TaxonomyId = Homologene.TaxonomyId
- """ % (escape(str(trait.geneid)), escape(dataset.group.name))
- logger.sql(query)
- result = g.db.execute(query).fetchone()
- #else:
- # result = None
-
- if result:
- trait.homologeneid = result[0]
-
description_string = unicode(str(trait.description).strip(codecs.BOM_UTF8), 'utf-8')
target_string = unicode(str(trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
@@ -582,47 +490,22 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
# Save it for the jinja2 template
trait.description_display = description_display
- #XZ: trait_location_value is used for sorting
trait.location_repr = 'N/A'
- trait.location_value = 1000000
-
if trait.chr and trait.mb:
- #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
- #This is so we can convert the location to a number used for sorting
- trait_location_value = convert_location_to_value(trait.chr, trait.mb)
- #try:
- # trait_location_value = int(self.chr)*1000 + self.mb
- #except ValueError:
- # if self.chr.upper() == 'X':
- # trait_location_value = 20*1000 + self.mb
- # else:
- # trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
- # self.mb)
-
- #ZS: Put this in function currently called "convert_location_to_value"
trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
- trait.location_value = trait_location_value
elif dataset.type == "Geno":
trait.location_repr = 'N/A'
- trait.location_value = 1000000
-
if trait.chr and trait.mb:
- #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
- #This is so we can convert the location to a number used for sorting
- trait_location_value = convert_location_to_value(trait.chr, trait.mb)
-
- #ZS: Put this in function currently called "convert_location_to_value"
trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
- trait.location_value = trait_location_value
if get_qtl_info:
#LRS and its location
trait.LRS_score_repr = "N/A"
- trait.LRS_score_value = 0
trait.LRS_location_repr = "N/A"
- trait.LRS_location_value = 1000000
+ trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
if dataset.type == 'ProbeSet' and not trait.cellid:
+ trait.mean = ""
query = """
SELECT
ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, ProbeSetXRef.mean, ProbeSetXRef.additive
@@ -653,9 +536,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
else:
trait.locus = trait.locus_chr = trait.locus_mb = trait.additive = ""
- else:
- trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.mean = trait.additive = ""
-
if dataset.type == 'Publish':
query = """
@@ -692,19 +572,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
trait.locus = trait.lrs = trait.additive = ""
if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
- #XZ: LRS_location_value is used for sorting
- try:
- LRS_location_value = int(trait.locus_chr)*1000 + float(trait.locus_mb)
- except:
- if trait.locus_chr.upper() == 'X':
- LRS_location_value = 20*1000 + float(trait.locus_mb)
- else:
- LRS_location_value = ord(str(trait.locus_chr).upper()[0])*1000 + float(trait.locus_mb)
-
trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
if trait.lrs != "":
trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
- trait.LRS_score_value = LRS_score_value = trait.lrs
else:
raise KeyError, `trait.name`+' information is not found in the database.'
diff --git a/wqflask/base/trait_collection.py b/wqflask/base/trait_collection.py
deleted file mode 100644
index d388a3af..00000000
--- a/wqflask/base/trait_collection.py
+++ /dev/null
@@ -1,53 +0,0 @@
-class TraitCollection(object):
-
- def __init__(self, is_anon=False):
- self.is_anon = is_anon
-
-
- @app.route("/collections/remove", methods=('POST',))
- def remove_traits():
- if is_anon:
- AnonCollection.remove_traits()
- else:
- UserCollection.remove_traits()
-
- params = request.form
- print("params are:", params)
- uc_id = params['uc_id']
- uc = model.UserCollection.query.get(uc_id)
- traits_to_remove = params.getlist('traits[]')
- print("traits_to_remove are:", traits_to_remove)
- traits_to_remove = process_traits(traits_to_remove)
- print("\n\n after processing, traits_to_remove:", traits_to_remove)
- all_traits = uc.members_as_set()
- print(" all_traits:", all_traits)
- members_now = all_traits - traits_to_remove
- print(" members_now:", members_now)
- print("Went from {} to {} members in set.".format(len(all_traits), len(members_now)))
- uc.members = json.dumps(list(members_now))
- uc.changed_timestamp = datetime.datetime.utcnow()
- db_session.commit()
-
- # We need to return something so we'll return this...maybe in the future
- # we can use it to check the results
- return str(len(members_now))
-
- def __init__(self, anon_id)
- self.anon_key = anon_key
- self.collection_members = Redis.smembers(self.anon_id)
- print("self.collection_members is:", self.collection_members)
- self.num_members = len(self.collection_members)
-
-
- @app.route("/collections/remove", methods=('POST',))
- def remove_traits(traits_to_remove):
- print("traits_to_remove:", traits_to_remove)
- for trait in traits_to_remove:
- Redis.srem(self.anon_id, trait)
- members_now = self.collection_members - traits_to_remove
- print("members_now:", members_now)
- print("Went from {} to {} members in set.".format(len(self.collection_members), len(members_now)))
-
- # We need to return something so we'll return this...maybe in the future
- # we can use it to check the results
- return str(len(members_now))
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index 845a7224..d8487f01 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -44,12 +44,12 @@ class webqtlCaseData(object):
def __repr__(self):
str = "<webqtlCaseData> "
- if self.value:
+ if self.value != None:
str += "value=%2.3f" % self.value
- if self.variance:
+ if self.variance != None:
str += " variance=%2.3f" % self.variance
if self.num_cases:
- str += " ndata=%d" % self.num_cases
+ str += " ndata=%s" % self.num_cases
if self.name:
str += " name=%s" % self.name
if self.name2:
@@ -66,14 +66,21 @@ class webqtlCaseData(object):
@property
def display_value(self):
- if self.value:
+ if self.value != None:
return "%2.3f" % self.value
else:
return "x"
@property
def display_variance(self):
- if self.variance:
+ if self.variance != None:
return "%2.3f" % self.variance
else:
return "x"
+
+ @property
+ def display_num_cases(self):
+ if self.num_cases != None:
+ return "%s" % self.num_cases
+ else:
+ return "x"
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index e5f10edf..018d5d54 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -20,45 +20,44 @@ USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
#minimum number of informative strains
KMININFORMATIVE = 5
-#maximum number of traits for interval mapping
-MULTIPLEMAPPINGLIMIT = 11
-
-#maximum number of traits for correlation
-MAXCORR = 100
-
#Daily download limit from one IP
DAILYMAXIMUM = 1000
#maximum LRS value
MAXLRS = 460.0
-#temporary data life span
-MAXLIFE = 86400
-
#MINIMUM Database public value
PUBLICTHRESH = 0
-#NBCI address
-NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=%s"
-UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgGene?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
-GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
-OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
-UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s";
-HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=homologene&Cmd=DetailsSearch&Term=%s"
+#EXTERNAL LINK ADDRESSES
PUBMEDLINK_URL = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=%s&dopt=Abstract"
-UCSC_POS = "http://genome.ucsc.edu/cgi-bin/hgTracks?clade=mammal&org=%s&db=%s&position=chr%s:%s-%s&pix=800&Submit=submit"
UCSC_BLAT = 'http://genome.ucsc.edu/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
UTHSC_BLAT = 'http://ucscbrowser.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
-UCSC_GENOME = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d&hgt.customText=http://web2qtl.utmem.edu:88/snp/chr%s"
-ENSEMBLE_BLAT = 'http://www.ensembl.org/Mus_musculus/featureview?type=AffyProbe&id=%s'
-DBSNP = 'http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s'
-UCSC_RUDI_TRACK_URL = " http://genome.cse.ucsc.edu/cgi-bin/hgTracks?org=%s&db=%s&hgt.customText=http://gbic.biol.rug.nl/~ralberts/tracks/%s/%s"
-GENOMEBROWSER_URL="http://ucscbrowser.genenetwork.org/cgi-bin/hgTracks?clade=mammal&org=Mouse&db=mm9&position=%s&hgt.suggest=&pix=800&Submit=submit"
-ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Lucene/Details?species=Mus_musculus;idx=Transcript;end=1;q=%s"
-
-# The following paths are no longer in use!
-# HTMLPATH is replaced by GENODIR
-# IMGDIR is replaced by GENERATED_IMAGE_DIR
+UTHSC_BLAT2 = 'http://ucscbrowserbeta.genenetwork.org/cgi-bin/hgBlat?org=%s&db=%s&type=0&sort=0&output=0&userSeq=%s'
+GENOMEBROWSER_URL="https://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=%s"
+NCBI_LOCUSID = "http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=%s"
+GENBANK_ID = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=search&doptcmdl=DocSum&term=%s"
+OMIM_ID = "http://www.ncbi.nlm.nih.gov/omim/%s"
+UNIGEN_ID = "http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s&CID=%s"
+HOMOLOGENE_ID = "http://www.ncbi.nlm.nih.gov/homologene/?term=%s"
+GENOTATION_URL = "http://www.genotation.org/Getd2g.pl?gene_list=%s"
+GTEX_URL = "https://www.gtexportal.org/home/gene/%s"
+GENEBRIDGE_URL = "https://www.systems-genetics.org/modules_by_gene/%s?organism=%s"
+GENEMANIA_URL = "https://genemania.org/search/%s/%s"
+UCSC_REFSEQ = "http://genome.cse.ucsc.edu/cgi-bin/hgTracks?db=%s&hgg_gene=%s&hgg_chrom=chr%s&hgg_start=%s&hgg_end=%s"
+BIOGPS_URL = "http://biogps.org/?org=%s#goto=genereport&id=%s"
+STRING_URL = "http://string-db.org/newstring_cgi/show_network_section.pl?identifier=%s"
+PANTHER_URL = "http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=%s"
+GEMMA_URL = "http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=%s"
+ABA_URL = "http://mouse.brain-map.org/search/show?search_type=gene&search_term=%s"
+EBIGWAS_URL = "https://www.ebi.ac.uk/gwas/search?query=%s"
+WIKI_PI_URL = "http://severus.dbmi.pitt.edu/wiki-pi/index.php/search?q=%s"
+ENSEMBLETRANSCRIPT_URL="http://useast.ensembl.org/Mus_musculus/Transcript/Idhistory?t=%s"
+DBSNP = 'http://ensembl.org/Mus_musculus/Variation/Population?v=%s'
+PROTEIN_ATLAS_URL = "http://www.proteinatlas.org/search/%s"
+OPEN_TARGETS_URL = "https://genetics.opentargets.org/gene/%s"
+UNIPROT_URL = "https://www.uniprot.org/uniprot/%s"
+RGD_URL = "https://rgd.mcw.edu/rgdweb/elasticResults.html?term=%s&category=Gene&species=%s"
# Temporary storage (note that this TMPDIR can be set as an
# environment variable - use utility.tools.TEMPDIR when you
@@ -70,8 +69,8 @@ assert_writable_dir(TMPDIR)
CACHEDIR = mk_dir(TMPDIR+'/cache/')
# We can no longer write into the git tree:
-GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'/generated/')
-GENERATED_TEXT_DIR = mk_dir(TMPDIR+'/generated_text/')
+GENERATED_IMAGE_DIR = mk_dir(TMPDIR+'generated/')
+GENERATED_TEXT_DIR = mk_dir(TMPDIR+'generated_text/')
# Make sure we have permissions to access these
assert_writable_dir(CACHEDIR)
@@ -81,6 +80,7 @@ assert_writable_dir(GENERATED_TEXT_DIR)
# Flat file directories
GENODIR = flat_files('genotype')+'/'
assert_dir(GENODIR)
+assert_dir(GENODIR+'bimbam') # for gemma
# JSON genotypes are OBSOLETE
JSON_GENODIR = flat_files('genotype/json')+'/'
@@ -92,4 +92,3 @@ if not valid_path(JSON_GENODIR):
PORTADDR = "http://50.16.251.170"
INFOPAGEHREF = '/dbdoc/%s.html'
CGIDIR = '/webqtl/' #XZ: The variable name 'CGIDIR' should be changed to 'PYTHONDIR'
-SCRIPTFILE = 'main.py'
diff --git a/wqflask/base/webqtlFormData.py b/wqflask/base/webqtlFormData.py
deleted file mode 100644
index 10251756..00000000
--- a/wqflask/base/webqtlFormData.py
+++ /dev/null
@@ -1,352 +0,0 @@
-# Copyright (C) University of Tennessee Health Science Center, Memphis, TN.
-#
-# This program is free software: you can redistribute it and/or modify it
-# under the terms of the GNU Affero General Public License
-# as published by the Free Software Foundation, either version 3 of the
-# License, or (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-# See the GNU Affero General Public License for more details.
-#
-# This program is available from Source Forge: at GeneNetwork Project
-# (sourceforge.net/projects/genenetwork/).
-#
-# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010)
-# at rwilliams@uthsc.edu and xzhou15@uthsc.edu
-#
-#
-#
-# This module is used by GeneNetwork project (www.genenetwork.org)
-#
-# Created by GeneNetwork Core Team 2010/08/10
-#
-# Last updated by GeneNetwork Core Team 2010/10/20
-
-#from mod_python import Cookie
-
-from __future__ import print_function
-from pprint import pformat as pf
-
-import string
-import os
-
-import reaper
-
-import webqtlConfig
-from webqtlCaseData import webqtlCaseData
-from utility import webqtlUtil
-
-class webqtlFormData(object):
- 'Represents data from a WebQTL form page, needed to generate the next page'
-
- attrs = ('formID','group','genotype','samplelist','allsamplelist', 'display_variance'
- 'suggestive','significance','submitID','identification', 'enablevariance',
- 'nperm','nboot','email','incparentsf1','genotype_1','genotype_2','traitInfo')
-
- #XZ: Attention! All attribute values must be picklable!
-
- def __init__(self,
- start_vars = None,
- req = None,
- mod_python_session=None,
- FieldStorage_formdata=None):
- # Todo: rework this whole thing
- print("in webqtlFormData start_vars are:", pf(start_vars))
- for item in webqtlFormData.attrs:
- self.__dict__[item] = None
-
- #ZS: This is only used in DataEditingPage.py (as far as I know)
- self.varianceDispName = None
-
- for item in start_vars:
- self.__dict__[item] = start_vars[item]
- print(" Now self.dict is:", pf(self.__dict__))
-
- #Todo: This can't be good below...rework
- try:
- self.remote_ip = req.connection.remote_ip
- except:
- self.remote_ip = '1.2.3.4'
-
- if req and req.headers_in.has_key('referer'):
- self.refURL = req.headers_in['referer']
- else:
- self.refURL = None
-
- # For now let's just comment all this out - Sam
-
- #self.cookies = cookieData.cookieData(Cookie.get_cookies(req)) #XZ: dictionary type. To hold values transfered from mod_python Cookie.
- #
- ##XZ: dictionary type. To hold values transfered from mod_python Session object. We assume that it is always picklable.
- #self.input_session_data = sessionData.sessionData( mod_python_session )
- #
- ##XZ: FieldStorage_formdata may contain item that can't be pickled. Must convert to picklable data.
- #self.formdata = cgiData( FieldStorage_formdata )
- #
- ##get Form ID
- #self.formID = self.formdata.getfirst('FormID')
- #
- ##get rest of the attributes
- #if self.formID:
- # for item in self.attrs:
- # value = self.formdata.getfirst(item)
- # if value != None:
- # setattr(self,item,string.strip(value))
-
- self.ppolar = None
- self.mpolar = None
-
- print("[yellow] self.group is:", self.group)
- if self.group:
- #try:
- # # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
- _f1, _f12, self.mpolar, self.ppolar = webqtlUtil.ParInfo[self.group]
- #except:
- # f1 = f12 = self.mpolar = self.ppolar = None
-
-
- def set_number(stringy):
- return int(stringy) if stringy else 2000 # Rob asked to change the default value to 2000
-
- self.nperm = set_number(self.nperm)
- self.nboot = set_number(self.nboot)
-
-
- #if self.allsamplelist:
- # self.allsamplelist = map(string.strip, string.split(self.allsamplelist))
- print("self.allsamplelist is:", self.allsamplelist)
- if self.allsamplelist:
- self.allsamplelist = self.allsamplelist.split()
- print("now self.allsamplelist is:", self.allsamplelist)
- #self.readGenotype()
- #self.readData()
-
- if self.group == 'BXD300':
- self.group = 'BXD'
-
-
- def __getitem__(self, key):
- print("in __getitem__")
- return self.__dict__[key]
-
- def get(self, key, default=None):
- if key in self.__dict__:
- return self.__dict__[key]
- else:
- return default
-
- def __str__(self):
- rstr = ''
- for item in self.attrs:
- if item != 'genotype':
- rstr += '%s:%s\n' % (item,str(getattr(self,item)))
- return rstr
-
-
- def readGenotype(self):
- '''read genotype from .geno file'''
- if self.group == 'BXD300':
- self.group = 'BXD'
-
- assert self.group, "self.group needs to be set"
-
- #genotype_1 is Dataset Object without parents and f1
- #genotype_2 is Dataset Object with parents and f1 (not for intercross)
-
- self.genotype_1 = reaper.Dataset()
-
- full_filename = locate(self.group + '.geno','genotype')
-
- # reaper barfs on unicode filenames, so here we ensure it's a string
- full_filename = str(full_filename)
- self.genotype_1.read(full_filename)
-
- print("Got to after read")
-
- try:
- # NL, 07/27/2010. ParInfo has been moved from webqtlForm.py to webqtlUtil.py;
- _f1, _f12, _mat, _pat = webqtlUtil.ParInfo[self.group]
- except KeyError:
- _f1 = _f12 = _mat = _pat = None
-
- self.genotype_2 = self.genotype_1
- if self.genotype_1.type == "group" and _mat and _pat:
- self.genotype_2 = self.genotype_1.add(Mat=_mat, Pat=_pat) #, F1=_f1)
-
- #determine default genotype object
- if self.incparentsf1 and self.genotype_1.type != "intercross":
- self.genotype = self.genotype_2
- else:
- self.incparentsf1 = 0
- self.genotype = self.genotype_1
-
- self.samplelist = list(self.genotype.prgy)
- self.f1list = []
- self.parlist = []
-
- if _f1 and _f12:
- self.f1list = [_f1, _f12]
- if _mat and _pat:
- self.parlist = [_mat, _pat]
-
-
- def readData(self, samplelist, incf1=None):
- '''read user input data or from trait data and analysis form'''
-
- if incf1 == None:
- incf1 = []
-
- if not self.genotype:
- self.readGenotype()
- if not samplelist:
- if incf1:
- samplelist = self.f1list + self.samplelist
- else:
- samplelist = self.samplelist
-
- #print("before traitfiledata self.traitfile is:", pf(self.traitfile))
-
- traitfiledata = getattr(self, "traitfile", None)
- traitpastedata = getattr(self, "traitpaste", None)
- variancefiledata = getattr(self, "variancefile", None)
- variancepastedata = getattr(self, "variancepaste", None)
- Nfiledata = getattr(self, "Nfile", None)
-
- #### Todo: Rewrite below when we get to someone submitting their own trait #####
-
- def to_float(item):
- try:
- return float(item)
- except ValueError:
- return None
-
- print("bottle samplelist is:", samplelist)
- if traitfiledata:
- tt = traitfiledata.split()
- values = map(webqtlUtil.StringAsFloat, tt)
- elif traitpastedata:
- tt = traitpastedata.split()
- values = map(webqtlUtil.StringAsFloat, tt)
- else:
- print("mapping formdataasfloat")
- #values = map(self.FormDataAsFloat, samplelist)
- values = [to_float(getattr(self, key)) for key in samplelist]
- print("rocket values is:", values)
-
-
- if len(values) < len(samplelist):
- values += [None] * (len(samplelist) - len(values))
- elif len(values) > len(samplelist):
- values = values[:len(samplelist)]
- print("now values is:", values)
-
-
- if variancefiledata:
- tt = variancefiledata.split()
- variances = map(webqtlUtil.StringAsFloat, tt)
- elif variancepastedata:
- tt = variancepastedata.split()
- variances = map(webqtlUtil.StringAsFloat, tt)
- else:
- variances = map(self.FormVarianceAsFloat, samplelist)
-
- if len(variances) < len(samplelist):
- variances += [None]*(len(samplelist) - len(variances))
- elif len(variances) > len(samplelist):
- variances = variances[:len(samplelist)]
-
- if Nfiledata:
- tt = string.split(Nfiledata)
- nsamples = map(webqtlUtil.IntAsFloat, tt)
- if len(nsamples) < len(samplelist):
- nsamples += [None]*(len(samplelist) - len(nsamples))
- else:
- nsamples = map(self.FormNAsFloat, samplelist)
-
- ##values, variances, nsamples is obsolete
- self.allTraitData = {}
- for i, _sample in enumerate(samplelist):
- if values[i] != None:
- self.allTraitData[_sample] = webqtlCaseData(
- _sample, values[i], variances[i], nsamples[i])
- print("allTraitData is:", pf(self.allTraitData))
-
-
-
- def informativeStrains(self, samplelist=None, include_variances = None):
- '''if readData was called, use this to output informative samples (sample with values)'''
-
- if not samplelist:
- samplelist = self.samplelist
-
- samples = []
- values = []
- variances = []
-
- #print("self.allTraitData is:", pf(self.allTraitData))
-
- for sample in samplelist:
- if sample in self.allTraitData:
- _val, _var = self.allTraitData[sample].value, self.allTraitData[sample].variance
- if _val != None:
- if include_variances:
- if _var != None:
- samples.append(sample)
- values.append(_val)
- variances.append(_var)
- else:
- samples.append(sample)
- values.append(_val)
- variances.append(None)
-
- return samples, values, variances, len(samples)
-
-
-
- #def FormDataAsFloat(self, key):
- #
- # #try:
- # # return float(self.key)
- # #except:
- # # return None
-
-
- def FormVarianceAsFloat(self, key):
- try:
- return float(self.formdata.getfirst('V' + key))
- except:
- return None
-
- def FormNAsFloat(self, key):
- try:
- return int(self.formdata.getfirst('N' + key))
- except:
- return None
-
- def Sample(self):
- 'Create some dummy data for testing'
- self.group = 'BXD'
- self.incparentsf1 = 'on'
- #self.display = 9.2
- #self.significance = 16.1
- self.readGenotype()
- self.identification = 'BXD : Coat color example by Lu Lu, et al'
- #self.readGenotype()
- #self.genotype.ReadMM('AXBXAforQTL')
- #self.samplelist = map((lambda x, y='': '%s%s' % (y,x)), self.genotype.prgy)
- #self.samplelist.sort()
- self.allTraitData = {'BXD29': webqtlCaseData(3), 'BXD28': webqtlCaseData(2),
- 'BXD25': webqtlCaseData(2), 'BXD24': webqtlCaseData(2), 'BXD27': webqtlCaseData(2),
- 'BXD21': webqtlCaseData(1), 'BXD20': webqtlCaseData(4), 'BXD23': webqtlCaseData(4),
- 'BXD22': webqtlCaseData(3), 'BXD14': webqtlCaseData(4), 'BXD15': webqtlCaseData(2),
- 'BXD16': webqtlCaseData(3), 'BXD11': webqtlCaseData(4), 'BXD12': webqtlCaseData(3),
- 'BXD13': webqtlCaseData(2), 'BXD18': webqtlCaseData(3), 'BXD19': webqtlCaseData(3),
- 'BXD38': webqtlCaseData(3), 'BXD39': webqtlCaseData(3), 'BXD36': webqtlCaseData(2),
- 'BXD34': webqtlCaseData(4), 'BXD35': webqtlCaseData(4), 'BXD32': webqtlCaseData(4),
- 'BXD33': webqtlCaseData(3), 'BXD30': webqtlCaseData(1), 'BXD31': webqtlCaseData(4),
- 'DBA/2J': webqtlCaseData(1), 'BXD8': webqtlCaseData(3), 'BXD9': webqtlCaseData(1),
- 'BXD6': webqtlCaseData(3), 'BXD5': webqtlCaseData(3), 'BXD2': webqtlCaseData(4),
- 'BXD1': webqtlCaseData(1), 'C57BL/6J': webqtlCaseData(4), 'B6D2F1': webqtlCaseData(4),
- 'BXD42': webqtlCaseData(4), 'BXD40': webqtlCaseData(3)}
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 22:05:40 +0000